After encountering gravitation fluctuations, Captain Janeway hails an approaching ship and meets its captain, Tash. He is working on a catapult vessel, hoping to launch himself hundreds of light-years away. If Tash's plan succeeds, it may shave years off the U.S.S. Voyager's journey. Meanwhile, Seven of Nine has installed a cortical processing subunit in her regeneration alcove, allowing her to assimilate the ships status reports. Upon downloading data on Tash's work, she informs Janeway that his catapult is the same technology that was used to trap them in the Delta Quadrant.

Five years ago, when Voyager was caught in the displacement wave that sent it 70,000 light years off course, a tetryon beam was responsible. Now, Seven has discovered that a tetryon reactor is powering the catapult. Although the Voyager crew believes they destroyed the reactor, Seven finds out otherwise. Data shows a charge Tuvok fired tore an opening in subspace, and a tractor beam from a cloaked ship pushed the reactor into it. Seven alerts Chakotay to her startling conclusion that Voyager was stranded in the Delta Quadrant on purpose and Janeway is behind it.

Seven believes the captain is part of a Federation conspiracy to establish a military presence in the Delta Quadrant. Suddenly, Janeway's diplomacy begins to look suspiciously like establishing tactical infrastructure. Seven believes the captain intends to use the catapult to bring more ships from the Alpha Quadrant, creating a Federation/Cardassian invasion force. When Tash makes a successful journey of 100 light years using the apparatus, Chakotay secretly delays Voyager's shield modification to give him more time to consider Seven's theories.

Seven returns to her alcove to assimilate for more information. After her latest download, she summons Janeway and alerts her that Chakotay is part of a Maquis rebellion. She believes he intends to use the catapult to launch attacks against the Federation and Cardassian ships. Janeway is doubtful, but Seven presents compelling theories, using some of the same evidence she used to cast aspersions on Janeway, but drawing different conclusions.

When Janeway and Chakotay compare notes, they realize Seven has been filling both of their minds with paranoid theories. Once the Doctor runs a diagnostic on her alcove, he finds that Seven has downloaded more information than she can process. Janeway beams to the Delta Flyer, which Seven is using to make a paranoid escape, and uses her own version of past events to convince Seven that her synaptic patterns are in chaos. They return to Voyager, and Seven is treated in sickbay.